Part:BBa_K5157108
60-2-N-A13S-SLE-PETase
Contents
Usage and Biology
IsPETase, a PET hydrolase discovered from the bacterium Ideonella sakaiensis 201-F6, has become a research favorite for its ability to efficiently degrade PET at low temperature [1]. It breaks PET into bis(2-hydroxyethyl) terephthalate (BHET) and 2-hydroxyethyl methyl terephthalate (MHET) by hydrolyzing the ester bond, followed by hydrolysis to the end products EG and TPA with the help of MHETase (Fig. 1). However, due to the surface hydrophobicity of PET, it is difficult for PETase to directly bind to it, which negatively affects the hydrolysis rate of PETase on PET [2].
Fig. 1. Schematic diagram of the PETase pathway for PET degradation.
Plastic-binding peptides are a class of short-chain peptides that can bind to PET plastic surfaces through hydrophobic binding and other forces, and are a potential solution to improve the degradability of PETase towards PET. However, the sources of PET-binding peptides are currently limited, and they are usually unearthed in a single-point trial-and-error manner, which is inefficient.
In this regard, firstly, we performed PET-binding peptide prediction with the help of deep learning, and, then, fused PETase with the efficient binding peptide obtained from the prediction and screening through linker to construct a fusion protein, so as to improve the binding ability of PETase to PET microplastics with the help of PET-binding peptide, thus improving the degradation efficiency.
We obtained short peptides with improved PET plastic binding ability (BBa_K5157093), but there is still room for improvement in the expression level of the fusion proteins and the microplastic substrate binding ability. Therefore, we used Mutcompute-super to introduce beneficial mutations at specific sites, to further improve the expression level of the fusion protein and the degradation ability of the microplastic substrate by molecular modification [4].
Our fusion proteins consist of four basic components:
1) PETase
IsPETase-derived modified mutant with high catalytic performance and stability.
2) SLE linker
3) PET-binding peptide
We used both LSTM and graph neural network (GCN) models to optimise the prediction of high-affinity to obtain efficient PET-binding peptides. For further improvement, we used Mutcompute-super to introduce beneficial mutations at specific sites of PET-binding peptide, and then used the extracted bioinformatics features as the input for the 3D deconvolutional neural network of Mutcompute-super. We then combined a machine learning classifier to predict the optimal amino acid mutation combination to optimize the protein's folding conformation, and further improved the degradation ability of the fusion protein towards PET substrate [4].
4) His tag
Fig. 2. Schematic diagram of the fusion protein gene expression cassette.
Molecular construction
The fusion protein gene was synthesised and cloned into plasmid pET-21b（with T7 promotor BBa_K4790075, lac operator BBa_K4790078, RBS BBa_K4790079, and T7 terminator BBa_K4790076) to construct recombinant plasmid pET21b-60-2-N-A13S-SLE-PETase-His tag.
Protein expression and purification
The recombinant plasmid was transformed into Escherichia coli BL21 (DE3) for expression and cultured in a 50 mL flask to express sufficient fusion protein.
After fermentation optimization with the fusion protein 50-4-N-G4S-PETase, we determined the final concentration of IPTG to be 0.05 mmol/L. After induction, the culture was incubated at 16°C and fermented for 48 h using TB medium. After culture, the fermentation broth was centrifuged, wall-broken by high-pressure homogenization, and then centrifuged again. The fermentation supernatant and supernatant of cell fragmentation were collected as the crude enzyme.
The crude enzyme activity was measured by continuous spectrophotometry method. The reaction system was 1500 μL including 30 μL 50 mmol/L pNPB, 30 μL crude enzyme liquid and 1440 μL 100 mmol/L pH 8.0 phosphate buffer. The generation rate of p-nitrophenol during 60 s was recorded at the wavelength of 405 nm. One enzyme activity unit (U) was defined as the amount of enzyme required to hydrolyze pNPB producing 1 μmol p-nitrophenol during 60 s at 60°C.
The crude enzyme liquid of the supernatant of cell fragmentation with higher enzyme activity was subjected to Ni2+ column affinity chromatography. After chromatography, the collected liquid was dialyzed, freeze-dried and re-solubilized. Then the obtained liquid is the pure enzyme solution. SDS-PAGE analysis showed that there was a clear band near 35 kDa (Fig. 3), indicating that the target fusion protein was successfully obtained after Ni2+ column affinity chromatography.
Fig. 3. SDS-PAGE analysis. M: Marker; FS: Fermentation supernatant; PC: Precipitation of cell fragmentation; SC: Supernatant of cell fragmentation; P: Purified enzyme.
Enzyme property characterization
1) Optimal pH
Enzyme activity was determined using phosphate buffer at 60°C 100 mmol/L pH 6.0-9.0 (gradient of 1.0). The relative enzyme activity at each pH was calculated using the highest enzyme activity measured as 100%. The enzyme activity of the fusion protein showed an increasing trend at pH 6.0-9.0, with the highest activity at pH 9.0 (Fig. 4).
Fig. 4. Optimum pH of 60-2-N-A13S-SLE-PETase.
2) Optimal temperature
The enzyme activity was determined by preheating the pH 8.0 phosphate buffer for 10 min at different temperatures (30, 40, 50, 60, 70°C). The highest enzyme activity measured was taken as 100% and the relative enzyme activity at each temperature was calculated. The enzyme activity of the fusion protein increased gradually with increasing temperature at 30-70°C (Fig. 5).
Fig. 5. Optimum temperature for 60-2-N-A13S-SLE-PETase.
3) Thermostability
The pure enzyme solution was placed in a 50°C water bath and sampled at 24 h intervals to determine the residual enzyme activity. The enzyme activity at 0 h of reaction was defined as 100%. The fusion protein didn’t possess good stability at 50°C reaction temperature (Fig. 6).
Fig. 6. Temperature stability for 60-2-N-A13S-SLE-PETase at 50°C.
Characterization of PET degradation property
PET microplastics (final concentration 2.9 g/L) were degraded by 0.01 mg/mL fusion protein under the condition of 100 mM glycine-NaOH buffer (pH 9.0) at 50°C. A total of 50 μL reaction liquid was taken mixing with 450 μL methanol after 24 h PET substrate degradation. After centrifugation, the supernatant was collected and filtered by aqueous phase filtration membrane, then the filtrate was analyzed by high performance liquid chromatography (HPLC).
Since BHET can be categorized as the incomplete degradation product of PET, and TPA and MHET can be categorized as the final degradation product of PET, we selected TPA and MHET as the indicators to calculate the product release. Compared with the original enzyme, the product release amount of 60-2-N-A13S-SLE-PETase was lower than PETase and 60-2-N-SLE-PETase. (Fig. 7).
Fig. 7. HPLC analysis of PET degradation of PETase and 60-2-N-A13S-SLE-PETase.
Introduction of point mutation to PET-binding peptide 60-2 negatively affected 60-2-N-SLE-PETase for PET degradation, so it was no longer used to superimpose the mutations in the next step.
References
[1] Yoshida S, Hiraga K, Takehana T, et al. A bacterium that degrades and assimilates poly(ethylene terephthalate) [J]. Science, 2016, 351(6278): 1196-1199.
[2] Puspitasari N, Tsai S L, Lee C K. Fungal hydrophobin RolA enhanced PETase hydrolysis of polyethylene terephthalate [J]. Applied Biochemistry and Biotechnology, 2021, 193(5): 1284-1295.
[3] Chen X, Zaro J L, Shen W C. Fusion protein linkers: property, design and functionality [J]. Advanced Drug Delivery Reviews, 2013, 65(10): 1357-1369.
[4] Deng Z H, Cai C,Wang S T, et al. A protein design method based on amino acid microenvironment and EMO neural network, CN118136092A [P/OL].
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal SpeI site found at 976
Illegal PstI site found at 157 - 12INCOMPATIBLE WITH RFC[12]Illegal SpeI site found at 976
Illegal PstI site found at 157
Illegal NotI site found at 115 - 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 839
- 23INCOMPATIBLE WITH RFC[23]Illegal SpeI site found at 976
Illegal PstI site found at 157 - 25INCOMPATIBLE WITH RFC[25]Illegal SpeI site found at 976
Illegal PstI site found at 157
Illegal NgoMIV site found at 367 - 1000COMPATIBLE WITH RFC[1000]
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